It is sometimes useful to hold all the animations of a layer inside the layer, rather than use expressions or parenting.
It is very useful when using the wiggle expression, for example, which changes whenever the amount of layers in a comp changes. Or when moving a layer in and out of a comp to change hierarchy.

You can solve parts of the problem in one of two ways:

  • Select a tranform property in a layer, then click Animation > Keyframe Assistant > Convert Expression to Keyframes. This will turn expressions to keyframes. Don't forget to remove the expression afterwards.
  • Bake Paranted Transform — This script, available through simply turns animation generated by either parenting or expressions into keyframes on the selected layer.

How to Bake Keyframes